H_S_S

I assembled a custom arduino board on a PCB with ATMega328AU. After burning the bootloader successfully through the IDE (I had to create a new entry with different device signature in avrdude.conf, but I managed it), the LED on pin 13 started blinking, which I think is a sign of the bootloader working. However, when I try to upload a program via FTDI I get the following message from the Arduino IDE:

System wide configuration file is "/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf" User configuration file is "/Users/Hristo/.avrduderc" User configuration file does not exist or is not a regular file, skipping